1
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Socarras KM, Marino MC, Earl JP, Ehrlich RL, Cramer NA, Mell JC, Sen B, Ahmed A, Marconi RT, Ehrlich GD. Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol. RESEARCH SQUARE 2024:rs.3.rs-4491589. [PMID: 38947078 PMCID: PMC11213207 DOI: 10.21203/rs.3.rs-4491589/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background The Borreliaceae family includes many obligate parasitic bacterial species which are etiologically associated with a myriad of zoonotic borrelioses including Lyme disease and vector-borne relapsing fevers. Infections by the Borreliaceae are difficult to detect by both direct and indirect methods, often leading to delayed and missed diagnoses. Efforts to improve diagnoses center around the development of molecular diagnostics (MDx), but due to deep tissue sequestration of the causative spirochaetes and the lack of persistent bacteremias, even MDx assays suffer from a lack of sensitivity. Additionally, the highly extensive genomic heterogeneity among isolates, even within the same species, contributes to the lack of assay sensitivity as single target assays cannot provide universal coverage. This within-species heterogeneity is partly due to differences in replicon repertoires and genomic structures that have likely arisen to support the complex Borreliaceae lifecycle in which these parasites have to survive in multiple hosts each with unique immune responses. Results We constructed a Borreliaceae family-level pangenome and characterized the phylogenetic relationships among the constituent taxa which supports the recent taxonomy of splitting the family into at least two genera. Gene content pro les were created for the majority of the Borreliaceae replicons, providing for the first time their unambiguous molecular typing. Conclusion Our characterization of the Borreliaceae pan-genome supports the splitting of the former Borrelia genus into two genera and provides for the phylogenetic placement of several non-species designated isolates. Mining this family-level pangenome will enable precision diagnostics corresponding to gene content-driven clinical outcomes while also providing targets for interventions.
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Affiliation(s)
- Kayla M Socarras
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Mary C Marino
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Joshua P Earl
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | | | - Nicholas A Cramer
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center
| | - Joshua C Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Bhaswati Sen
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Azad Ahmed
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Richard T Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center
| | - Garth D Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
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2
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Morales-Espinosa R, Delgado G, Espinosa-Camacho F, Flores-Alanis A, Rodriguez C, Mendez JL, Gonzalez-Pedraza A, Cravioto A. Pseudomonas aeruginosa strains isolated from animal with high virulence genes content and highly sensitive to antimicrobials. J Glob Antimicrob Resist 2024; 37:75-80. [PMID: 38452900 DOI: 10.1016/j.jgar.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVES P. aeruginosa is one of the most metabolically versatile bacteria having the ability to survive in multiple environments through its accessory genome. An important hallmark of P. aeruginosa is the high level of antibiotic resistance, which often makes eradication difficult and sometimes impossible. Evolutionary forces have led to this bacterium to develop high antimicrobial resistance with a variety of elements contributing to both intrinsic and acquired resistance. The objectives were to genetically and phenotypically characterizer P. aeruginosa strains isolated from companion animals of different species. METHODS We characterized a collection of 39 P. aeruginosa strains isolated from infected animals. The genetic characterization was in relation to chromosomal profile by PFGE; content of virulence gene; presence of genomic islands (GIs); genes of the cytotoxins exported by T3SS: exoU, exoS, exoT and exoY; and type IV pili allele. The phenotypic characterization was based on patterns of susceptibility to different antimicrobials. RESULTS Each strain had a PFGE profile, a high virulence genes content, and a large accessory genome. However, most of the strains presented high sensitivity to almost all antimicrobials tested, showing no acquired resistance (no β-lactamases). The exception to this lack of resistance was seen with penicillin. CONCLUSIONS P. aeruginosa could be a naturally sensitive bacterium to standard antimicrobials but could rapidly develop intrinsic and acquired resistance when the bacterium is exposed to pressure exerted by antibiotics, as observed in hospital settings.
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Affiliation(s)
- Rosario Morales-Espinosa
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.
| | - Gabriela Delgado
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Fernando Espinosa-Camacho
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alejandro Flores-Alanis
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Cristina Rodriguez
- Bacteriology Laboratory, Faculty of Veterinary, Universidad Nacional Autónoma de México., Coyoacán, Ciudad de México, México
| | - Jose L Mendez
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alberto Gonzalez-Pedraza
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alejandro Cravioto
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
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3
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Aroca Molina KJ, Gutiérrez SJ, Benítez-Campo N, Correa A. Genomic Differences Associated with Resistance and Virulence in Pseudomonas aeruginosa Isolates from Clinical and Environmental Sites. Microorganisms 2024; 12:1116. [PMID: 38930498 PMCID: PMC11205572 DOI: 10.3390/microorganisms12061116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 06/28/2024] Open
Abstract
Pseudomonas aeruginosa is a pathogen that causes healthcare-associated infections (HAIs) worldwide. It is unclear whether P. aeruginosa isolated from the natural environment has the same pathogenicity and antimicrobial resistance potential as clinical strains. In this study, virulence- and resistance-associated genes were compared in 14 genomic sequences of clinical and environmental isolates of P. aeruginosa using the VFDB, PATRIC, and CARD databases. All isolates were found to share 62% of virulence genes related to adhesion, motility, secretion systems, and quorum sensing and 72.9% of resistance genes related to efflux pumps and membrane permeability. Our results indicate that both types of isolates possess conserved genetic information associated with virulence and resistance mechanisms regardless of the source. However, none of the environmental isolates were associated with high-risk clones (HRCs). These clones (ST235 and ST111) were found only in clinical isolates, which have an impact on human medical epidemiology due to their ability to spread and persist, indicating a correlation between the clinical environment and increased virulence. The genomic variation and antibiotic susceptibility of environmental isolates of P. aeruginosa suggest potential biotechnological applications if obtained from sources that are under surveillance and investigation to limit the emergence and spread of antibiotic resistant strains.
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Affiliation(s)
- Kelly J. Aroca Molina
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Sonia Jakeline Gutiérrez
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Neyla Benítez-Campo
- Department of Biology, Faculty of Natural and Exact Sciences, Universidad del Valle, Cali 760042, Colombia; (K.J.A.M.); (S.J.G.)
| | - Adriana Correa
- Department of Basic Sciences, Universidad Santiago de Cali, Cali 760035, Colombia;
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4
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Ambreetha S, Zincke D, Balachandar D, Mathee K. Genomic and metabolic versatility of Pseudomonas aeruginosa contributes to its inter-kingdom transmission and survival. J Med Microbiol 2024; 73. [PMID: 38362900 DOI: 10.1099/jmm.0.001791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
Pseudomonas aeruginosa is one of the most versatile bacteria with renowned pathogenicity and extensive drug resistance. The diverse habitats of this bacterium include fresh, saline and drainage waters, soil, moist surfaces, taps, showerheads, pipelines, medical implants, nematodes, insects, plants, animals, birds and humans. The arsenal of virulence factors produced by P. aeruginosa includes pyocyanin, rhamnolipids, siderophores, lytic enzymes, toxins and polysaccharides. All these virulent elements coupled with intrinsic, adaptive and acquired antibiotic resistance facilitate persistent colonization and lethal infections in different hosts. To date, treating pulmonary diseases remains complicated due to the chronic secondary infections triggered by hospital-acquired P. aeruginosa. On the contrary, this bacterium can improve plant growth by suppressing phytopathogens and insects. Notably, P. aeruginosa is one of the very few bacteria capable of trans-kingdom transmission and infection. Transfer of P. aeruginosa strains from plant materials to hospital wards, animals to humans, and humans to their pets occurs relatively often. Recently, we have identified that plant-associated P. aeruginosa strains could be pathologically similar to clinical isolates. In this review, we have highlighted the genomic and metabolic factors that facilitate the dominance of P. aeruginosa across different biological kingdoms and the varying roles of this bacterium in plant and human health.
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Affiliation(s)
- Sakthivel Ambreetha
- Developmental Biology and Genetics, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Diansy Zincke
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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5
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Bourdin T, Benoit MÈ, Bédard E, Prévost M, Quach C, Déziel E, Constant P. High-Throughput Short Sequence Typing Schemes for Pseudomonas aeruginosa and Stenotrophomonas maltophilia Pure Culture and Environmental DNA. Microorganisms 2023; 12:48. [PMID: 38257875 PMCID: PMC10819370 DOI: 10.3390/microorganisms12010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Molecular typing techniques are utilized to determine genetic similarities between bacterial isolates. However, the use of environmental DNA profiling to assess epidemiologic links between patients and their environment has not been fully explored. This work reports the development and validation of two high-throughput short sequence typing (HiSST) schemes targeting the opportunistic pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia, along with a modified SM2I selective medium for the specific isolation of S. maltophilia. These HiSST schemes are based on four discriminative loci for each species and demonstrate high discriminating power, comparable to pairwise whole-genome comparisons. Each scheme includes species-specific PCR primers for precise differentiation from closely related taxa, without the need for upstream culture-dependent methods. For example, the primers targeting the bvgS locus make it possible to distinguish P. aeruginosa from the very closely related Pseudomonas paraeruginosa sp. nov. The selected loci included in the schemes are adapted to massive parallel amplicon sequencing technology. An R-based script implemented in the DADA2 pipeline was assembled to facilitate HiSST analyses for efficient and accurate genotyping of P. aeruginosa and S. maltophilia. We demonstrate the performance of both schemes through in silico validations, assessments against reference culture collections, and a case study involving environmental samples.
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Affiliation(s)
- Thibault Bourdin
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| | - Marie-Ève Benoit
- CHU Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; (M.-È.B.); (C.Q.)
| | - Emilie Bédard
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada; (E.B.); (M.P.)
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada; (E.B.); (M.P.)
| | - Caroline Quach
- CHU Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; (M.-È.B.); (C.Q.)
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| | - Philippe Constant
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
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6
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Mugunthan S, Wong LL, Winnerdy FR, Summers S, Bin Ismail MH, Foo YH, Jaggi TK, Meldrum OW, Tiew PY, Chotirmall SH, Rice SA, Phan AT, Kjelleberg S, Seviour T. RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms. Nat Commun 2023; 14:7772. [PMID: 38012164 PMCID: PMC10682433 DOI: 10.1038/s41467-023-43533-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
The extracellular matrix of bacterial biofilms consists of diverse components including polysaccharides, proteins and DNA. Extracellular RNA (eRNA) can also be present, contributing to the structural integrity of biofilms. However, technical difficulties related to the low stability of RNA make it difficult to understand the precise roles of eRNA in biofilms. Here, we show that eRNA associates with extracellular DNA (eDNA) to form matrix fibres in Pseudomonas aeruginosa biofilms, and the eRNA is enriched in certain bacterial RNA transcripts. Degradation of eRNA associated with eDNA led to a loss of eDNA fibres and biofilm viscoelasticity. Compared with planktonic and biofilm cells, the biofilm matrix was enriched in specific mRNA transcripts, including lasB (encoding elastase). The mRNA transcripts colocalised with eDNA fibres in the biofilm matrix, as shown by single molecule inexpensive FISH microscopy (smiFISH). The lasB mRNA was also observed in eDNA fibres in a clinical sputum sample positive for P. aeruginosa. Thus, our results indicate that the interaction of specific mRNAs with eDNA facilitates the formation of viscoelastic networks in the matrix of Pseudomonas aeruginosa biofilms.
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Affiliation(s)
- Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Stephen Summers
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- St John's Island National Marine Laboratory c/o Tropical Marine Science Institute, National University of Singapore, 119227, Singapore
| | | | - Yong Hwee Foo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), Nanyang Technological University, Singapore, 636921, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Oliver W Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- The iThree Institute, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Canberra, Australia
| | - Anh Tuân Phan
- School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Aarhus, 8000, Denmark.
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7
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Chandler CE, Hofstaedter CE, Hazen TH, Rasko DA, Ernst RK. Genomic and Functional Characterization of Longitudinal Pseudomonas aeruginosa Isolates from Young Patients with Cystic Fibrosis. Microbiol Spectr 2023; 11:e0155623. [PMID: 37358436 PMCID: PMC10433850 DOI: 10.1128/spectrum.01556-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/05/2023] [Indexed: 06/27/2023] Open
Abstract
Individuals with cystic fibrosis (CF) suffer from frequent and recurring microbial airway infections. The Gram-negative bacterium Pseudomonas aeruginosa is one of the most common organisms isolated from CF patient airways. P. aeruginosa establishes chronic infections that persist throughout a patient's lifetime and is a major cause of morbidity and mortality. Throughout the course of infection, P. aeruginosa must evolve and adapt from an initial state of early, transient colonization to chronic colonization of the airways. Here, we examined isolates of P. aeruginosa from children under the age of 3 years old with CF to determine genetic adaptations the bacterium undergoes during this early stage of colonization and infection. These isolates were collected when early aggressive antimicrobial therapy was not the standard of care and therefore highlight strain evolution under limited antibiotic pressure. Examination of specific phenotypic adaptations, such as lipid A palmitoylation, antibiotic resistance, and loss of quorum sensing, did not reveal a clear genetic basis for such changes. Additionally, we demonstrate that the geography of patient origin, within the United States or among other countries, does not appear to significantly influence genetic adaptation. In summary, our results support the long-standing model that patients acquire individual isolates of P. aeruginosa that subsequently become hyperadapted to the patient-specific airway environment. This study provides a multipatient genomic analysis of isolates from young CF patients in the United States and contributes data regarding early colonization and adaptation to the growing body of research about P. aeruginosa evolution in the context of CF airway disease. IMPORTANCE Chronic lung infection with Pseudomonas aeruginosa is of major concern for patients with cystic fibrosis (CF). During infection, P. aeruginosa undergoes genomic and functional adaptation to the hyperinflammatory CF airway, resulting in worsening lung function and pulmonary decline. All studies that describe these adaptations use P. aeruginosa obtained from older children or adults during late chronic lung infection; however, children with CF can be infected with P. aeruginosa as early as 3 months of age. Therefore, it is unclear when these genomic and functional adaptations occur over the course of CF lung infection, as access to P. aeruginosa isolates in children during early infection is limited. Here, we present a unique cohort of CF patients who were identified as being infected with P. aeruginosa at an early age prior to aggressive antibiotic therapy. Furthermore, we performed genomic and functional characterization of these isolates to address whether chronic CF P. aeruginosa phenotypes are present during early infection.
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Affiliation(s)
- Courtney E. Chandler
- Department of Microbial Pathogenesis, University of Maryland—Baltimore, Baltimore, Maryland, USA
| | - Casey E. Hofstaedter
- Department of Microbial Pathogenesis, University of Maryland—Baltimore, Baltimore, Maryland, USA
- Medical Scientist Training Program, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tracy H. Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland—Baltimore, Baltimore, Maryland, USA
| | - David A. Rasko
- Department of Microbial Pathogenesis, University of Maryland—Baltimore, Baltimore, Maryland, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland—Baltimore, Baltimore, Maryland, USA
- Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland—Baltimore, Baltimore, Maryland, USA
- Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
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8
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Horspool AM, Sen-Kilic E, Malkowski AC, Breslow SL, Mateu-Borras M, Hudson MS, Nunley MA, Elliott S, Ray K, Snyder GA, Miller SJ, Kang J, Blackwood CB, Weaver KL, Witt WT, Huckaby AB, Pyles GM, Clark T, Al Qatarneh S, Lewis GK, Damron FH, Barbier M. Development of an anti- Pseudomonas aeruginosa therapeutic monoclonal antibody WVDC-5244. Front Cell Infect Microbiol 2023; 13:1117844. [PMID: 37124031 PMCID: PMC10140502 DOI: 10.3389/fcimb.2023.1117844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/22/2023] [Indexed: 05/02/2023] Open
Abstract
The rise of antimicrobial-resistant bacterial infections is a crucial health concern in the 21st century. In particular, antibiotic-resistant Pseudomonas aeruginosa causes difficult-to-treat infections associated with high morbidity and mortality. Unfortunately, the number of effective therapeutic interventions against antimicrobial-resistant P. aeruginosa infections continues to decline. Therefore, discovery and development of alternative treatments are necessary. Here, we present pre-clinical efficacy studies on an anti-P. aeruginosa therapeutic monoclonal antibody. Using hybridoma technology, we generated a monoclonal antibody and characterized its binding to P. aeruginosa in vitro using ELISA and fluorescence correlation spectroscopy. We also characterized its function in vitro and in vivo against P. aeruginosa. The anti-P. aeruginosa antibody (WVDC-5244) bound P. aeruginosa clinical strains of various serotypes in vitro, even in the presence of alginate exopolysaccharide. In addition, WVDC-5244 induced opsonophagocytic killing of P. aeruginosa in vitro in J774.1 murine macrophage, and complement-mediated killing. In a mouse model of acute pneumonia, prophylactic administration of WVDC-5244 resulted in an improvement of clinical disease manifestations and reduction of P. aeruginosa burden in the respiratory tract compared to the control groups. This study provides promising pre-clinical efficacy data on a new monoclonal antibody with therapeutic potential for P. aeruginosa infections.
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Affiliation(s)
- Alexander M. Horspool
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Emel Sen-Kilic
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Aaron C. Malkowski
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Scott L. Breslow
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Margalida Mateu-Borras
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Matthew S. Hudson
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Mason A. Nunley
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Sean Elliott
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Krishanu Ray
- University of Maryland, Baltimore School of Medicine, Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, United States
| | - Greg A. Snyder
- University of Maryland, Baltimore School of Medicine, Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, United States
| | - Sarah Jo Miller
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Jason Kang
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Catherine B. Blackwood
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Kelly L. Weaver
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - William T. Witt
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Annalisa B. Huckaby
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Gage M. Pyles
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Tammy Clark
- Department of Pediatrics, Division of Cystic Fibrosis, West Virginia University, Morgantown, WV, United States
| | - Saif Al Qatarneh
- Department of Pediatrics, Division of Cystic Fibrosis, West Virginia University, Morgantown, WV, United States
| | - George K. Lewis
- University of Maryland, Baltimore School of Medicine, Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, United States
| | - F. Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, WV, United States
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9
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Lin S, Chen S, Li L, Cao H, Li T, Hu M, Liao L, Zhang LH, Xu Z. Genome characterization of a uropathogenic Pseudomonas aeruginosa isolate PA_HN002 with cyclic di-GMP-dependent hyper-biofilm production. Front Cell Infect Microbiol 2022; 12:956445. [PMID: 36004331 PMCID: PMC9394441 DOI: 10.3389/fcimb.2022.956445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa can cause various types of infections and is one of the most ubiquitous antibiotic-resistant pathogens found in healthcare settings. It is capable of adapting to adverse conditions by transforming its motile lifestyle to a sessile biofilm lifestyle, which induces a steady state of chronic infection. However, mechanisms triggering the lifestyle transition of P. aeruginosa strains with clinical significance are not very clear. In this study, we reported a recently isolated uropathogenic hyper-biofilm producer PA_HN002 and characterized its genome to explore genetic factors that may promote its transition into the biofilm lifestyle. We first showed that high intracellular c-di-GMP content in PA_HN002 gave rise to its attenuated motilities and extraordinary strong biofilm. Reducing the intracellular c-di-GMP content by overexpressing phosphodiesterases (PDEs) such as BifA or W909_14950 converted the biofilm and motility phenotypes. Whole genome sequencing and comprehensive analysis of all the c-di-GMP metabolizing enzymes led to the identification of multiple mutations within PDEs. Gene expression assays further indicated that the shifted expression profile of c-di-GMP metabolizing enzymes in PA_HN002 might mainly contribute to its elevated production of intracellular c-di-GMP and enhanced biofilm formation. Moreover, mobile genetic elements which might interfere the endogenous regulatory network of c-di-GMP metabolism in PA_HN002 were analyzed. This study showed a reprogrammed expression profile of c-di-GMP metabolizing enzymes which may promote the pathoadaption of clinical P. aeruginosa into biofilm producers.
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Affiliation(s)
- Siying Lin
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Li Li
- Women and Children’s Health Institute, Guangdong Women and Children Hospital, Guangzhou, China
- *Correspondence: Li Li, ; Zeling Xu,
| | - Huiluo Cao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ting Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Ming Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lisheng Liao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- *Correspondence: Li Li, ; Zeling Xu,
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10
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Sacco MD, Defrees K, Zhang X, Lawless W, Nwanochie E, Balsizer A, Darch SE, Renslo AR, Chen Y. Structure-Based Ligand Design Targeting Pseudomonas aeruginosa LpxA in Lipid A Biosynthesis. ACS Infect Dis 2022; 8:1231-1240. [PMID: 35653508 DOI: 10.1021/acsinfecdis.1c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymes involved in lipid A biosynthesis are promising antibacterial drug targets in Gram-negative bacteria. In this study, we use a structure-based design approach to develop a series of novel tetrazole ligands with low μM affinity for LpxA, the first enzyme in the lipid A pathway. Aided by previous structural data, X-ray crystallography, and surface plasmon resonance bioanalysis, we identify 17 hit compounds. Two of these hits were subsequently modified to optimize interactions with three regions of the LpxA active site. This strategy ultimately led to the discovery of ligand L13, which had a KD of 3.0 μM. The results reveal new chemical scaffolds as potential LpxA inhibitors, important binding features for ligand optimization, and protein conformational changes in response to ligand binding. Specifically, they show that a tetrazole ring is well-accommodated in a small cleft formed between Met169, the "hydrophobic-ruler" and His156, both of which demonstrate significant conformational flexibility. Furthermore, we find that the acyl-chain binding pocket is the most tractable region of the active site for realizing affinity gains and, along with a neighboring patch of hydrophobic residues, preferentially binds aliphatic and aromatic groups. The results presented herein provide valuable chemical and structural information for future inhibitor discovery against this important antibacterial drug target.
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Affiliation(s)
- Michael D. Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94143, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - William Lawless
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Emeka Nwanochie
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Amelia Balsizer
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Sophie E. Darch
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94143, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
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11
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Verhoeve VI, Brammer JA, Driscoll TP, Kambouris AR, Rasko DA, Cross AS, Gillespie JJ. Genome sequencing of Pseudomonas aeruginosa strain M2 illuminates traits of an opportunistic pathogen of burn wounds. G3 (BETHESDA, MD.) 2022; 12:jkac073. [PMID: 35348684 PMCID: PMC9073672 DOI: 10.1093/g3journal/jkac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/02/2022] [Indexed: 01/28/2023]
Abstract
Pseudomonas aeruginosa is a Gram-negative nosocomial pathogen and one of the most prevalent organisms isolated from burn wounds worldwide. Pseudomonas aeruginosa strain M2 (O5 serotype, type B flagella) is utilized for examining the murine model associated with burns. Pseudomonas aeruginosa M2 is similar in lethality to common laboratory P. aeruginosa strains when infecting CD-1 mice. Conversely, we recently showed that, relative to these strains, P. aeruginosa M2-infected mice are more susceptible to sepsis and demonstrate a 6-log reduction in LD50 from subcutaneous infection at the infection site directly after 10% total body surface area burn. To better understand this striking phenotypic difference from other P. aeruginosa strains employed in burn models, we sequenced the P. aeruginosa M2 genome. A total of 4,136,641 read pairs were obtained, providing an average genome coverage of 97.5X; subsequent assembly yielded a draft genome with 187 contigs comprising 6,360,304 bp with a G + C content of 66.45%. Genome-based phylogeny estimation of 92 P. aeruginosa strains placed P. aeruginosa M2 with P. aeruginosa-12-4-4(59), a nonairway clinical strain isolated from the blood culture of a burn patient. Phylogenomic analyses identified genes shared between P. aeruginosa M2 and P. aeruginosa 14, another strain exhibiting increased lethality in thermal tissues, as well as P. aeruginosa M2 unique genes with diverse functions like degradation of toxic aromatic compounds, iron scavenging, swarming motility and biofilm formation, defense against invasive DNA, and host assault. Predicted lateral gene transfers illuminate proteins heretofore uncharacterized for roles in P. aeruginosa biology. Our work yields a rich resource for assessing P. aeruginosa genes required for increased lethality in burn tissue seroma.
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Affiliation(s)
- Victoria I Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jerod A Brammer
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Timothy P Driscoll
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Adrienne R Kambouris
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alan S Cross
- Center for Vaccine Development, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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12
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Lichtenberg M, Jakobsen TH, Kühl M, Kolpen M, Jensen PØ, Bjarnsholt T. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6574409. [PMID: 35472245 PMCID: PMC9438473 DOI: 10.1093/femsre/fuac018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/04/2022] [Accepted: 04/24/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2200, København, Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2200, København, Denmark
| | - Thomas Bjarnsholt
- Corresponding author: Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark. Tel: +45 20659888; E-mail:
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13
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Galeb S, Zaki MES, Shrief R, Hassan R, Rizk M. Diagnostic Value of Multiplex Polymerase Chain Reaction in Detection of Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia from Sepsis in Pediatrics. Recent Pat Biotechnol 2021; 15:195-203. [PMID: 34825643 DOI: 10.2174/1872208315666210719104623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/10/2021] [Accepted: 05/27/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Proper identification of the causative organism in pediatric sepsis is crucial for early diagnosis and prevention of septic shock and organ failure. OBJECTIVES The aim of the present study was to evaluate the multiplex polymerase chain reaction (PCR) for detection of Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia from positive blood cultures for these pathogens isolated from children with hospital- acquired sepsis compared to the conventional biochemical reactions for identification of these organisms. METHODS This study was a cross-sectional study performed on 100 isolates from pediatric blood cultures, including Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia. The study also included 100 isolates of Escherichia coli as a negative control. All isolates were identified by API 20NE and the multiplex PCR with primers specific to the 3 tested bacteria. RESULTS Multiplex PCR was positive in 96% of isolates and 4 isolates had negative results. Falsepositive results were reported with three E. coli strains. Multiplex PCR identified all the isolates of Acinetobacter baumannii, 29 isolates of Pseudomonas aeruginosa and 27 isolates of Stenotrophomonas maltophilia. The diagnostic value of the multiplex PCR compared to the biochemical identification revealed sensitivity 96.04%, specificity 96.9%, positive predictive value 97.00%, negative predictive value 96.00% and accuracy 96.50%. CONCLUSION The present study highlights the diagnostic value of multiplex PCR to identify Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia from positive blood cultures. Multiplex PCR was sensitive, specific and accurate. The accuracy differs according to the organisms with 100% accuracy for Acinetobacter baumannii.
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Affiliation(s)
- Sara Galeb
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Maysaa El Sayed Zaki
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Raghdaa Shrief
- Medical Microbiology and Immunology Department, Faculty of Medicine, Damietta University, New Damietta, Egypt
| | - Rasha Hassan
- Pediatric Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Mohamed Rizk
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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14
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Ambreetha S, Marimuthu P, Mathee K, Balachandar D. Rhizospheric and endophytic Pseudomonas aeruginosa in edible vegetable plants share molecular and metabolic traits with clinical isolates. J Appl Microbiol 2021; 132:3226-3248. [PMID: 34608722 DOI: 10.1111/jam.15317] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/28/2021] [Accepted: 09/21/2021] [Indexed: 01/02/2023]
Abstract
AIM Pseudomonas aeruginosa, a leading opportunistic pathogen causing hospital-acquired infections, is also commonly found in agricultural settings. However, there are minimal attempts to examine the molecular and functional attributes shared by agricultural and clinical strains of P. aeruginosa. This study investigates the presence of P. aeruginosa in edible vegetable plants (including salad vegetables) and analyses the evolutionary and metabolic relatedness of the agricultural and clinical strains. METHODS AND RESULTS Eighteen rhizospheric and endophytic P. aeruginosa strains were isolated from cucumber, tomato, eggplant, and chili directly from the farms. The identity of these strains was confirmed using biochemical and molecular assays. The genetic and metabolic traits of these plant-associated P. aeruginosa isolates were compared with clinical strains. DNA fingerprinting and 16S rDNA-based phylogenetic analyses revealed that the plant- and human-associated strains are evolutionarily related. Both agricultural and clinical isolates possessed plant-beneficial properties, including mineral solubilization to release essential nutrients (phosphorous, potassium, and zinc), ammonification, and the ability to release extracellular pyocyanin, siderophore, and indole-3 acetic acid. CONCLUSION These findings suggest that rhizospheric and endophytic P. aeruginosa strains are genetically and functionally analogous to the clinical isolates. In addition, the genotypic and phenotypic traits do not correlate with plant sources or ecosystems. SIGNIFICANCE AND IMPACT OF THE STUDY This study reconfirms that edible plants are the potential source for human and animal transmission of P. aeruginosa.
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Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.,Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
| | - Ponnusamy Marimuthu
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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15
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Socarras KM, Earl JP, Krol JE, Bhat A, Pabilonia M, Harrison MH, Lang SP, Sen B, Ahmed A, Hester M, Mell JC, Vandegrift K, Ehrlich GD. Species-Level Profiling of Ixodes pacificus Bacterial Microbiomes Reveals High Variability Across Short Spatial Scales at Different Taxonomic Resolutions. Genet Test Mol Biomarkers 2021; 25:551-562. [PMID: 34406842 DOI: 10.1089/gtmb.2021.0088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background and Aims: Outbreaks of severe and chronic tick-borne diseases (TBDs) are on the rise. This is through the transmission of infectious disease agents to humans during tick feeding. The transmission rate and extent of microbial exchange, however, vary based on the tick microbiome composition. While select microbes are determined to be members of the normal tick microbiome and others are clearly recognized mammalian and/or avian pathogens, the status of many other members of the tick microbiota with respect to human and alternate host pathogenesis remains unclear. Moreover, the species-level 16S microbiome of prominent TBD vectors, including Ixodes pacificus, have not been extensively studied. To elucidate the I. pacificus microbiome composition, we performed a pan-domain species-specific characterization of the bacterial microbiome on adult I. pacificus ticks collected from two regional parks within Western California. Our methods provide for characterizing nuances within cohort microbiomes and their relationships to geo-locale of origin, surrounding fauna, and prevalences of known and suspected pathogens in relation to current TBD epidemiological zones. Methods: Ninety-two adult I. pacificus bacterial microbiomes were characterized using a high-fidelity, pan-domain, species-specific, full-length 16S rRNA amplification method using circular consensus sequencing performed on the Pacific Biosciences Sequel platform. Data analyses were performed with the MCSMRT data analysis package and database. Results: The species-specific I. pacificus microbiome composition illustrates a complex assortment of microflora, including over 900 eubacterial species with high taxonomic diversity, which was revealed to vary by sex and geo-locale, though the use of full-length 16S gene sequencing. The TBD-associated pathogens, such as Borrelia burgdorferi, Anaplasma phagocytophilum, and Rickettsia monacensis, were identified along with a host of bacteria previously unassociated with ticks. Conclusion: Species-level taxonomic classification of the I. pacificus microbiome revealed that full-length bacterial 16S gene sequencing is required for the granularity to elucidate the microbial diversity within and among ticks based on geo-locale.
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Affiliation(s)
- Kayla M Socarras
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Microbiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Joshua P Earl
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Microbiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Jaroslaw E Krol
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Microbiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Archana Bhat
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Max Pabilonia
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Haverford College, Haverford, Pennsylvania, USA
| | - Meghan H Harrison
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,College of Engineering and Natural Sciences, University of Tulsa, Tulsa, Oklahoma, USA
| | - Steven P Lang
- Exosome Diagnostics, a Bio-Techne Company, Waltham, Massachusetts, USA
| | - Bhaswati Sen
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Microbiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Azad Ahmed
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Microbiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael Hester
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Joshua Chang Mell
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Microbiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Kurt Vandegrift
- Department of Biology, Center for Infectious Disease Dynamics, Penn State University; University Park, Pennsylvania, USA
| | - Garth D Ehrlich
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Microbiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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16
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Del Mar Cendra M, Torrents E. Differential adaptability between reference strains and clinical isolates of Pseudomonas aeruginosa into the lung epithelium intracellular lifestyle. Virulence 2021; 11:862-876. [PMID: 32697923 PMCID: PMC7549915 DOI: 10.1080/21505594.2020.1787034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Intracellular invasion is an advantageous mechanism used by pathogens to evade host defense and antimicrobial therapy. In patients, the intracellular microbial lifestyle can lead to infection persistence and recurrence, thus worsening outcomes. Lung infections caused by Pseudomonas aeruginosa, especially in cystic fibrosis (CF) patients, are often aggravated by intracellular invasion and persistence of the pathogen. Proliferation of the infectious species relies on a continuous deoxyribonucleotide (dNTP) supply, for which the ribonucleotide reductase enzyme (RNR) is the unique provider. The large genome plasticity of P. aeruginosa and its ability to rapidly adapt to different environments are challenges for studying the pathophysiology associated with this type of infection. Using different reference strains and clinical isolates of P. aeruginosa independently combined with alveolar (A549) and bronchial (16HBE14o- and CF-CFBE41o-) epithelial cells, we analyzed host-pathogen interactions and intracellular bacterial persistence with the aim of determining a cell type-directed infection promoted by the P. aeruginosa strains. The oscillations in cellular toxicity and oxygen consumption promoted by the intracellular persistence of the strains were also analyzed among the different infectious lung models. Significantly, we identified class II RNR as the enzyme that supplies dNTPs to intracellular P. aeruginosa. This discovery could contribute to the development of RNR-targeted strategies against the chronicity occurring in this type of lung infection. Overall our study demonstrates that the choice of bacterial strain is critical to properly study the type of infectious process with relevant translational outcomes.
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Affiliation(s)
- Maria Del Mar Cendra
- Bacterial Infections and Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Science and Technology , Barcelona, Spain
| | - Eduard Torrents
- Bacterial Infections and Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Science and Technology , Barcelona, Spain.,Microbiology Section, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona , Barcelona, Spain
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17
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M. Abd Asada M, Aziz Mahal Al-amri N. Molecular identification and Virulence factors of Pseudomonas aeruginosa isolated from operation hall. AL-KUFA UNIVERSITY JOURNAL FOR BIOLOGY 2021; 13:39-46. [DOI: 10.36320/ajb/v13.i2.11758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This study aimed to determine the P.aeruginosa that causes contamination to operation hall in hospitals by detecting of pathogenisity markers ..Moreover, the virulence factors of predominant species were detected phenotypically by using routine techniques, that responsible for pathogenicity.
Fifteen samples were collected from different sites of operation hall during two months 2022 in AL-Hussein hospital/ karbala City. The identification of P.aeruginosa isolates depended on colonial morphology, microscopic examination and biochemical tests as a primary identification. The final identification was confirm by PCR technique from different sites .The results obtained by the PCR tests were twenty two isolates of P.aeruginosa were detected , which distributed into :(9) earth, (8) wall, and (10) beds.
The study investigated the virulence factors of P.aeruginosa, which had the ability to produce capsule, biofilm , adhesion ,protease, bacteriocin ,haemolysin and β-lactamase and gelatinase .
The results revealed variation in the resistance of bacteria to some antibiotics,..P.aeruginosa exhibited high resistance (96%) to Cefotaxime, but absolute susceptibility to Ciproflaxacin and Gentamycin and high susceptibility to Amikacin.Ceftiaxone,and Azithromycin.
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18
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Yoon EJ, Jeong SH. Mobile Carbapenemase Genes in Pseudomonas aeruginosa. Front Microbiol 2021; 12:614058. [PMID: 33679638 PMCID: PMC7930500 DOI: 10.3389/fmicb.2021.614058] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa is one of the major concerns in clinical settings impelling a great challenge to antimicrobial therapy for patients with infections caused by the pathogen. While membrane permeability, together with derepression of the intrinsic beta-lactamase gene, is the global prevailing mechanism of carbapenem resistance in P. aeruginosa, the acquired genes for carbapenemases need special attention because horizontal gene transfer through mobile genetic elements, such as integrons, transposons, plasmids, and integrative and conjugative elements, could accelerate the dissemination of the carbapenem-resistant P. aeruginosa. This review aimed to illustrate epidemiologically the carbapenem resistance in P. aeruginosa, including the resistance rates worldwide and the carbapenemase-encoding genes along with the mobile genetic elements responsible for the horizontal dissemination of the drug resistance determinants. Moreover, the modular mobile elements including the carbapenemase-encoding gene, also known as the P. aeruginosa resistance islands, are scrutinized mostly for their structures.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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19
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Hammond JA, Gordon EA, Socarras KM, Chang Mell J, Ehrlich GD. Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis. Biochem Soc Trans 2020; 48:2437-2455. [PMID: 33245329 PMCID: PMC7752077 DOI: 10.1042/bst20190713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023]
Abstract
The principle of monoclonality with regard to bacterial infections was considered immutable prior to 30 years ago. This view, espoused by Koch for acute infections, has proven inadequate regarding chronic infections as persistence requires multiple forms of heterogeneity among the bacterial population. This understanding of bacterial plurality emerged from a synthesis of what-were-then novel technologies in molecular biology and imaging science. These technologies demonstrated that bacteria have complex life cycles, polymicrobial ecologies, and evolve in situ via the horizontal exchange of genic characters. Thus, there is an ongoing generation of diversity during infection that results in far more highly complex microbial communities than previously envisioned. This perspective is based on the fundamental tenet that the bacteria within an infecting population display genotypic diversity, including gene possession differences, which result from horizontal gene transfer mechanisms including transformation, conjugation, and transduction. This understanding is embodied in the concepts of the supragenome/pan-genome and the distributed genome hypothesis (DGH). These paradigms have fostered multiple researches in diverse areas of bacterial ecology including host-bacterial interactions covering the gamut of symbiotic relationships including mutualism, commensalism, and parasitism. With regard to the human host, within each of these symbiotic relationships all bacterial species possess attributes that contribute to colonization and persistence; those species/strains that are pathogenic also encode traits for invasion and metastases. Herein we provide an update on our understanding of bacterial plurality and discuss potential applications in diagnostics, therapeutics, and vaccinology based on perspectives provided by the DGH with regard to the evolution of pathogenicity.
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Affiliation(s)
- Jocelyn A. Hammond
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Emma A. Gordon
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Kayla M. Socarras
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Joshua Chang Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
- Department of Otolaryngology – Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, U.S.A
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20
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Ng J, Guo F, Marneth AE, Ghanta S, Kwon MY, Keegan J, Liu X, Wright KT, Kamaz B, Cahill LA, Mullally A, Perrella MA, Lederer JA. Augmenting emergency granulopoiesis with CpG conditioned mesenchymal stromal cells in murine neutropenic sepsis. Blood Adv 2020; 4:4965-4979. [PMID: 33049055 PMCID: PMC7556132 DOI: 10.1182/bloodadvances.2020002556] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022] Open
Abstract
Patients with immune deficiencies from cancers and associated treatments represent a growing population within the intensive care unit with increased risk of morbidity and mortality from sepsis. Mesenchymal stromal cells (MSCs) are an integral part of the hematopoietic niche and express toll-like receptors, making them candidate cells to sense and translate pathogenic signals into an innate immune response. In this study, we demonstrate that MSCs administered therapeutically in a murine model of radiation-associated neutropenia have dual actions to confer a survival benefit in Pseudomonas aeruginosa pneumo-sepsis that is not from improved bacterial clearance. First, MSCs augment the neutrophil response to infection, an effect that is enhanced when MSCs are preconditioned with CpG oligodeoxynucleotide, a toll-like receptor 9 agonist. Using cytometry by time of flight, we identified proliferating neutrophils (Ly6GlowKi-67+) as the main expanded cell population within the bone marrow. Further analysis revealed that CpG-MSCs expand a lineage restricted progenitor population (Lin-Sca1+C-kit+CD150-CD48+) in the bone marrow, which corresponded to a doubling in the myeloid proliferation and differentiation potential in response to infection compared with control. Despite increased neutrophils, no reduction in organ bacterial count was observed between experimental groups. However, the second effect exerted by CpG-MSCs is to attenuate organ damage, particularly in the lungs. Neutrophils obtained from irradiated mice and cocultured with CpG-MSCs had decreased neutrophil extracellular trap formation, which was associated with decreased citrullinated H3 staining in the lungs of mice given CpG-MSCs in vivo. Thus, this preclinical study provides evidence for the therapeutic potential of MSCs in neutropenic sepsis.
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Affiliation(s)
- Julie Ng
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | | | | | - Min-Young Kwon
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Xiaoli Liu
- Division of Pulmonary and Critical Care, Department of Medicine
- Department of Pediatric Newborn Medicine, and
| | - Kyle T Wright
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | | | | | - Mark A Perrella
- Division of Pulmonary and Critical Care, Department of Medicine
- Department of Pediatric Newborn Medicine, and
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21
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Nolan LM, Turnbull L, Katrib M, Osvath SR, Losa D, Lazenby JJ, Whitchurch CB. Pseudomonas aeruginosa is capable of natural transformation in biofilms. MICROBIOLOGY (READING, ENGLAND) 2020; 166:995-1003. [PMID: 32749953 PMCID: PMC7660920 DOI: 10.1099/mic.0.000956] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/11/2020] [Indexed: 12/28/2022]
Abstract
Natural transformation is a mechanism that enables competent bacteria to acquire naked, exogenous DNA from the environment. It is a key process that facilitates the dissemination of antibiotic resistance and virulence determinants throughout bacterial populations. Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that produces large quantities of extracellular DNA (eDNA) that is required for biofilm formation. P. aeruginosa has a remarkable level of genome plasticity and diversity that suggests a high degree of horizontal gene transfer and recombination but is thought to be incapable of natural transformation. Here we show that P. aeruginosa possesses homologues of all proteins known to be involved in natural transformation in other bacterial species. We found that P. aeruginosa in biofilms is competent for natural transformation of both genomic and plasmid DNA. Furthermore, we demonstrate that type-IV pili (T4P) facilitate but are not absolutely essential for natural transformation in P. aeruginosa.
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Affiliation(s)
- Laura M. Nolan
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
- National Heart and Lung Institute, Imperial College London, London, SW3 6LR, UK
| | - Lynne Turnbull
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Marilyn Katrib
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Sarah R. Osvath
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
| | - Davide Losa
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
- Present address: Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, TN 38123, Italy
| | - James J. Lazenby
- Microbes in the Food Chain Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Cynthia B. Whitchurch
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia
- Microbes in the Food Chain Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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22
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Gasparrini AJ, Markley JL, Kumar H, Wang B, Fang L, Irum S, Symister CT, Wallace M, Burnham CAD, Andleeb S, Tolia NH, Wencewicz TA, Dantas G. Tetracycline-inactivating enzymes from environmental, human commensal, and pathogenic bacteria cause broad-spectrum tetracycline resistance. Commun Biol 2020; 3:241. [PMID: 32415166 PMCID: PMC7229144 DOI: 10.1038/s42003-020-0966-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/17/2020] [Indexed: 12/19/2022] Open
Abstract
Tetracycline resistance by antibiotic inactivation was first identified in commensal organisms but has since been reported in environmental and pathogenic microbes. Here, we identify and characterize an expanded pool of tet(X)-like genes in environmental and human commensal metagenomes via inactivation by antibiotic selection of metagenomic libraries. These genes formed two distinct clades according to habitat of origin, and resistance phenotypes were similarly correlated. Each gene isolated from the human gut encodes resistance to all tetracyclines tested, including eravacycline and omadacycline. We report a biochemical and structural characterization of one enzyme, Tet(X7). Further, we identify Tet(X7) in a clinical Pseudomonas aeruginosa isolate and demonstrate its contribution to tetracycline resistance. Lastly, we show anhydrotetracycline and semi-synthetic analogues inhibit Tet(X7) to prevent enzymatic tetracycline degradation and increase tetracycline efficacy against strains expressing tet(X7). This work improves our understanding of resistance by tetracycline-inactivation and provides the foundation for an inhibition-based strategy for countering resistance.
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Affiliation(s)
- Andrew J Gasparrini
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jana L Markley
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Hirdesh Kumar
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Luting Fang
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Sidra Irum
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Chanez T Symister
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Meghan Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Carey-Ann D Burnham
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Saadia Andleeb
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Niraj H Tolia
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | | | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Biomedical Engineering, Washington University, St. Louis, MO, 63130, USA.
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23
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Magalhães AP, Jorge P, Pereira MO. Pseudomonas aeruginosa and Staphylococcus aureus communication in biofilm infections: insights through network and database construction. Crit Rev Microbiol 2019; 45:712-728. [DOI: 10.1080/1040841x.2019.1700209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Andreia Patrícia Magalhães
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Paula Jorge
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Maria Olívia Pereira
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
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24
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Fleiszig SMJ, Kroken AR, Nieto V, Grosser MR, Wan SJ, Metruccio MME, Evans DJ. Contact lens-related corneal infection: Intrinsic resistance and its compromise. Prog Retin Eye Res 2019; 76:100804. [PMID: 31756497 DOI: 10.1016/j.preteyeres.2019.100804] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 12/20/2022]
Abstract
Contact lenses represent a widely utilized form of vision correction with more than 140 million wearers worldwide. Although generally well-tolerated, contact lenses can cause corneal infection (microbial keratitis), with an approximate annualized incidence ranging from ~2 to ~20 cases per 10,000 wearers, and sometimes resulting in permanent vision loss. Research suggests that the pathogenesis of contact lens-associated microbial keratitis is complex and multifactorial, likely requiring multiple conspiring factors that compromise the intrinsic resistance of a healthy cornea to infection. Here, we outline our perspective of the mechanisms by which contact lens wear sometimes renders the cornea susceptible to infection, focusing primarily on our own research efforts during the past three decades. This has included studies of host factors underlying the constitutive barrier function of the healthy cornea, its response to bacterial challenge when intrinsic resistance is not compromised, pathogen virulence mechanisms, and the effects of contact lens wear that alter the outcome of host-microbe interactions. For almost all of this work, we have utilized the bacterium Pseudomonas aeruginosa because it is the leading cause of lens-related microbial keratitis. While not yet common among corneal isolates, clinical isolates of P. aeruginosa have emerged that are resistant to virtually all currently available antibiotics, leading the United States CDC (Centers for Disease Control) to add P. aeruginosa to its list of most serious threats. Compounding this concern, the development of advanced contact lenses for biosensing and augmented reality, together with the escalating incidence of myopia, could portent an epidemic of vision-threatening corneal infections in the future. Thankfully, technological advances in genomics, proteomics, metabolomics and imaging combined with emerging models of contact lens-associated P. aeruginosa infection hold promise for solving the problem - and possibly life-threatening infections impacting other tissues.
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Affiliation(s)
- Suzanne M J Fleiszig
- School of Optometry, University of California, Berkeley, CA, USA; Graduate Group in Vision Science, University of California, Berkeley, CA, USA; Graduate Groups in Microbiology and Infectious Diseases & Immunity, University of California, Berkeley, CA, USA.
| | - Abby R Kroken
- School of Optometry, University of California, Berkeley, CA, USA
| | - Vincent Nieto
- School of Optometry, University of California, Berkeley, CA, USA
| | | | - Stephanie J Wan
- Graduate Group in Vision Science, University of California, Berkeley, CA, USA
| | | | - David J Evans
- School of Optometry, University of California, Berkeley, CA, USA; College of Pharmacy, Touro University California, Vallejo, CA, USA
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25
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Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites. Sci Rep 2018; 8:15668. [PMID: 30353070 PMCID: PMC6199293 DOI: 10.1038/s41598-018-34020-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.
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26
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Bricio-Moreno L, Sheridan VH, Goodhead I, Armstrong S, Wong JKL, Waters EM, Sarsby J, Panagiotou S, Dunn J, Chakraborty A, Fang Y, Griswold KE, Winstanley C, Fothergill JL, Kadioglu A, Neill DR. Evolutionary trade-offs associated with loss of PmrB function in host-adapted Pseudomonas aeruginosa. Nat Commun 2018; 9:2635. [PMID: 29980663 PMCID: PMC6035264 DOI: 10.1038/s41467-018-04996-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 06/06/2018] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas aeruginosa colonises the upper airway of cystic fibrosis (CF) patients, providing a reservoir of host-adapted genotypes that subsequently establish chronic lung infection. We previously experimentally-evolved P. aeruginosa in a murine model of respiratory tract infection and observed early-acquired mutations in pmrB, encoding the sensor kinase of a two-component system that promoted establishment and persistence of infection. Here, using proteomics, we show downregulation of proteins involved in LPS biosynthesis, antimicrobial resistance and phenazine production in pmrB mutants, and upregulation of proteins involved in adherence, lysozyme resistance and inhibition of the chloride ion channel CFTR, relative to wild-type strain LESB65. Accordingly, pmrB mutants are susceptible to antibiotic treatment but show enhanced adherence to airway epithelial cells, resistance to lysozyme treatment, and downregulate host CFTR expression. We propose that P. aeruginosa pmrB mutations in CF patients are subject to an evolutionary trade-off, leading to enhanced colonisation potential, CFTR inhibition, and resistance to host defences, but also to increased susceptibility to antibiotics.
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Affiliation(s)
- Laura Bricio-Moreno
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Victoria H Sheridan
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Ian Goodhead
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 3GL, UK
| | - Janet K L Wong
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Elaine M Waters
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
- Department of Microbiology, School of Natural Science, National University of Ireland, Galway, H91 TK33, Ireland
| | - Joscelyn Sarsby
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Stavros Panagiotou
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - James Dunn
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Adrita Chakraborty
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Yongliang Fang
- Thayer School of Engineering, Dartmouth, Hanover, NH, 03755, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, 03755, USA
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK.
| | - Aras Kadioglu
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Daniel R Neill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK.
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27
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Chen JW, Lau YY, Krishnan T, Chan KG, Chang CY. Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques. Front Microbiol 2018; 9:1104. [PMID: 29892277 PMCID: PMC5985333 DOI: 10.3389/fmicb.2018.01104] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.
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Affiliation(s)
- Jian-Woon Chen
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yin Yin Lau
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Thiba Krishnan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Chien-Yi Chang
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
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28
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Rossitto M, Fiscarelli EV, Rosati P. Challenges and Promises for Planning Future Clinical Research Into Bacteriophage Therapy Against Pseudomonas aeruginosa in Cystic Fibrosis. An Argumentative Review. Front Microbiol 2018; 9:775. [PMID: 29780361 PMCID: PMC5945972 DOI: 10.3389/fmicb.2018.00775] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 04/05/2018] [Indexed: 01/16/2023] Open
Abstract
Although early aggressive and prolonged treatment with specific antibiotics can extend survival in patients with cystic fibrosis (CF) colonized by opportunistic Pseudomonas aeruginosa (PA), antibiotics fail to eradicate the infecting multidrug-resistant (MDR) PA strains in CF. Century-long research has suggested treating patients with bacteriophages (phages, prokaryotic viruses) naturally hosted by bacteria. Although the only phage types used in therapy, lytic phages, lyse PA aggregated in biofilm matrix by depolymerase degrading enzymes, how they can effectively, safely, and persistently do so in patients with CF is unclear. Even though advanced techniques for formulating phage cocktails, training phages and collecting phage libraries have improved efficacy in vitro, whether personalized or ready-to-use therapeutic approaches or phages and antibiotics combined are effective and safe in vivo, and can reduce PA biofilms, remains debatable. Hence, to advance clinical research on phage therapy in clinical trials, also involving mucoid and non-mucoid multidrug-resistant PA in CF, and overcome problems in Western international regulations, we need reliable and repeatable information from experiments in vitro and in vivo on phage characterization, cocktail selection, personalized approaches, and phages combined with antibiotics. These findings, challenges, and promises prompted us to undertake this argumentative review to seek up-to-date information from papers describing lytic phage activity tested in vitro on PA laboratory strains, and PA strains from chronic infections including CF. We also reviewed in vivo studies on phage activity on pulmonary and non-pulmonary animal host models infected by laboratory or CF PA strains. Our argumentative review provides essential information showing that future phage clinical research in CF should use well-characterized and selected phages isolated against CF PA, tested in vitro under dynamic conditions in cocktails or combined with antibiotics, and in vivo on non-pulmonary and pulmonary host models infected with mucoid and non-mucoid CF MDR PA. Our findings should encourage pharmaceutical industries to conduct clinical trials in vitro and in vivo testing patented genomic engineered phages from phage libraries combined with antibiotics to treat or even prevent multidrug-resistant PA in CF, thus helping international regulatory agencies to plan future clinical research on phage therapy in CF.
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Affiliation(s)
- Martina Rossitto
- Cystic Fibrosis Microbiology, Laboratory Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Ersilia V. Fiscarelli
- Cystic Fibrosis Microbiology, Laboratory Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Paola Rosati
- Unit of Clinical Epidemiology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
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29
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Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients. mSphere 2018; 3:mSphere00615-17. [PMID: 29564400 PMCID: PMC5853491 DOI: 10.1128/msphere.00615-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/08/2018] [Indexed: 11/22/2022] Open
Abstract
Patients with cystic fibrosis endure “chronic focal infections” with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P. aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P. aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents—a phenomenon we define as “heterogeneous MICs.” By sequencing pairs of P. aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair mechanisms, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications. Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability. Pseudomonas aeruginosa isolates from CF patients have long been recognized for their overall reduced rate of antimicrobial susceptibility, but their intraclonal MIC heterogeneity has long been overlooked. Using two distinct cohorts of clinical strains (n = 224 from 56 CF patients, n = 130 from 68 non-CF patients) isolated in 2013, we demonstrated profound Etest MIC heterogeneity in CF P. aeruginosa isolates in comparison to non-CF P. aeruginosa isolates. On the basis of whole-genome sequencing of 19 CF P. aeruginosa isolates from 9 patients with heterogeneous MICs, the core genome phylogenetic tree confirmed the within-patient CF P. aeruginosa clonal lineage along with considerable coding sequence variability. No extrachromosomal DNA elements or previously characterized antibiotic resistance mutations could account for the wide divergence in antimicrobial MICs between P. aeruginosa coisolates, though many heterogeneous mutations in efflux and porin genes and their regulators were present. A unique OprD sequence was conserved among the majority of isolates of CF P. aeruginosa analyzed, suggesting a pseudomonal response to selective pressure that is common to the isolates. Genomic sequence data also suggested that CF pseudomonal hypermutability was not entirely due to mutations in mutL, mutS, and uvr. We conclude that the net effect of hundreds of adaptive mutations, both shared between clonally related isolate pairs and unshared, accounts for their highly heterogeneous MIC variances. We hypothesize that this heterogeneity is indicative of the pseudomonal syntrophic-like lifestyle under conditions of being “locked” inside a host focal airway environment for prolonged periods. IMPORTANCE Patients with cystic fibrosis endure “chronic focal infections” with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P. aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P. aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents—a phenomenon we define as “heterogeneous MICs.” By sequencing pairs of P. aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair machinery, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications.
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Morales-Espinosa R, Delgado G, Espinosa LF, Isselo D, Méndez JL, Rodriguez C, Miranda G, Cravioto A. Fingerprint Analysis and Identification of Strains ST309 as a Potential High Risk Clone in a Pseudomonas aeruginosa Population Isolated from Children with Bacteremia in Mexico City. Front Microbiol 2017; 8:313. [PMID: 28298909 PMCID: PMC5331068 DOI: 10.3389/fmicb.2017.00313] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and is associated with nosocomial infections. Its ability to thrive in a broad range of environments is due to a large and diverse genome of which its accessory genome is part. The objective of this study was to characterize P. aeruginosa strains isolated from children who developed bacteremia, using pulse-field gel electrophoresis, and in terms of its genomic islands, virulence genes, multilocus sequence type, and antimicrobial susceptibility. Our results showed that P. aeruginosa strains presented the seven virulence genes: toxA, lasB, lecA, algR, plcH, phzA1, and toxR, a type IV pilin alleles (TFP) group I or II. Additionally, we detected a novel pilin and accessory gene, expanding the number of TFP alleles to group VI. All strains presented the PAPI-2 Island and the majority were exoU+ and exoS+ genotype. Ten percent of the strains were multi-drug resistant phenotype, 18% extensively drug-resistant, 68% moderately resistant and only 3% were susceptible to all the antimicrobial tested. The most prevalent acquired β-Lactamase was KPC. We identified a group of ST309 strains, as a potential high risk clone. Our finding also showed that the strains isolated from patients with bacteremia have important virulence factors involved in colonization and dissemination as: a TFP group I or II; the presence of the exoU gene within the PAPI-2 island and the presence of the exoS gene.
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Affiliation(s)
- Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Gabriela Delgado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Luis F Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Dassaev Isselo
- Servicio de Pediatría, Hospital Regional 36 San Alejandro, IMSS Puebla, Mexico
| | - José L Méndez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Cristina Rodriguez
- Laboratorio de Bacteriología, Facultad de Veterinaria y Zootecnia, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Guadalupe Miranda
- Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Unidad de Investigación en Epidemiología Hospitalaria Mexico City, Mexico
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Woo TE, Duong J, Jervis NM, Rabin HR, Parkins MD, Storey DG. Virulence adaptations of Pseudomonas aeruginosa isolated from patients with non-cystic fibrosis bronchiectasis. MICROBIOLOGY-SGM 2016; 162:2126-2135. [PMID: 27902425 DOI: 10.1099/mic.0.000393] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pseudomonas aeruginosa is a major pathogen in chronic lung diseases such as cystic fibrosis (CF) and non-cystic fibrosis bronchiectasis (nCFB). Much of our understanding regarding infections in nCFB patients is extrapolated from findings in CF with little direct investigation on the adaptation of P. aeruginosa in nCFB patients. As such, we investigated whether the adaptation of P. aeruginosa was indeed similar between nCFB and CF. From our prospectively collected biobank, we identified 40 nCFB patients who had repeated P. aeruginosa isolates separated by ≥6 months and compared these to a control population of 28 CF patients. A total of 84 nCFB isolates [40 early (defined as the earliest isolate in the biobank) and 41 late (defined as the last available isolate in the biobank)] were compared to 83 CF isolates (39 early and 44 late). We assessed the isolates for protease, lipase and elastase production; mucoid phenotype; swarm and swim motility; biofilm production; and the presence of the lasR mutant phenotype. Overall, we observed phenotypic heterogeneity in both nCFB and CF isolates and found that P. aeruginosa adapted to the nCFB lung environment similarly to the way observed in CF isolates in terms of protease and elastase expression, motility and biofilm formation. However, significant differences between nCFB and CF isolates were observed in lipase expression, which may allude to distinct characteristics found in the lung environment of nCFB patients. We also sought to determine virulence potential over time in nCFB P. aeruginosa isolates and found that virulence decreased over time, similar to CF.
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Affiliation(s)
- Taylor E Woo
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Jessica Duong
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Nicole M Jervis
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Harvey R Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.,Department of Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.,Department of Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Douglas G Storey
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.,Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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Nair AV, Joseph N, Krishna K, Sneha KG, Tom N, Jangid K, Nair S. A comparative study of coastal and clinical isolates of Pseudomonas aeruginosa. Braz J Microbiol 2015; 46:725-34. [PMID: 26413053 PMCID: PMC4568853 DOI: 10.1590/s1517-838246320140502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 12/19/2014] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium having a versatile metabolic potential and great ecological and clinical significance. The geographical distribution of P. aeruginosahas revealed the existence of an unbiased genetic arrangement in terrestrial isolates. In contrast, there are very few reports about P. aeruginosa strains from marine environments. The present work was aimed at studying the distribution of P. aeruginosa in coastal waters along the Indian Peninsula and understanding the environmental influence on genotypic, metabolic and phenotypic characteristics by comparing marine and clinical isolates. Of the 785 marine isolates obtained on selective media, only 32 (~4.1%) were identified as P. aeruginosa, based on their fatty acid methyl ester profiles. A low Euclidian distance value (< 2.5) obtained from chemotaxonomic analysis suggested that all the environmental (coastal and marine) isolates originated from a single species. While UPGMA analyses of AP-PCR and phenotypic profiles separated the environmental and clinical isolates, fatty acid biotyping showed overlapping between most clinical and environmental isolates. Our study revealed the genetic diversity among different environmental isolates of P. aeruginosa. While biogeographical separation was not evident based solely on phenotypic and metabolic typing, genomic and metatranscriptomic studies are more likely to show differences between these isolates. Thus, newer and more insightful methods are required to understand the ecological distribution of this complex group of bacteria.
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Affiliation(s)
- Anusree V. Nair
- Central Marine Fisheries Research Institute, Indian Council of
Agricultural Research, Kochi, India
| | - Neetha Joseph
- Microbial Culture Collection, National Centre for Cell Science, Pune,
India
| | - Kiran Krishna
- Council of Scientific and Industrial Research, National Institute of
Oceanography, Kochi, India
| | - K. G. Sneha
- Council of Scientific and Industrial Research, National Institute of
Oceanography, Kochi, India
| | - Neenu Tom
- Council of Scientific and Industrial Research, National Institute of
Oceanography, Kochi, India
| | - Kamlesh Jangid
- Microbial Culture Collection, National Centre for Cell Science, Pune,
India
| | - Shanta Nair
- Council of Scientific and Industrial Research, National Institute of
Oceanography, Panjim, India
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The prrF-encoded small regulatory RNAs are required for iron homeostasis and virulence of Pseudomonas aeruginosa. Infect Immun 2014; 83:863-75. [PMID: 25510881 DOI: 10.1128/iai.02707-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that requires iron to cause infection, but it also must regulate the uptake of iron to avoid iron toxicity. The iron-responsive PrrF1 and PrrF2 small regulatory RNAs (sRNAs) are part of P. aeruginosa's iron regulatory network and affect the expression of at least 50 genes encoding iron-containing proteins. The genes encoding the PrrF1 and PrrF2 sRNAs are encoded in tandem in P. aeruginosa, allowing for the expression of a distinct, heme-responsive sRNA named PrrH that appears to regulate genes involved in heme metabolism. Using a combination of growth, mass spectrometry, and gene expression analysis, we showed that the ΔprrF1,2 mutant, which lacks expression of the PrrF and PrrH sRNAs, is defective for both iron and heme homeostasis. We also identified phuS, encoding a heme binding protein involved in heme acquisition, and vreR, encoding a previously identified regulator of P. aeruginosa virulence genes, as novel targets of prrF-mediated heme regulation. Finally, we showed that the prrF locus encoding the PrrF and PrrH sRNAs is required for P. aeruginosa virulence in a murine model of acute lung infection. Moreover, we showed that inoculation with a ΔprrF1,2 deletion mutant protects against future challenge with wild-type P. aeruginosa. Combined, these data demonstrate that the prrF-encoded sRNAs are critical regulators of P. aeruginosa virulence.
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Rhoads DD, Sintchenko V, Rauch CA, Pantanowitz L. Clinical microbiology informatics. Clin Microbiol Rev 2014; 27:1025-47. [PMID: 25278581 PMCID: PMC4187636 DOI: 10.1128/cmr.00049-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future.
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Affiliation(s)
- Daniel D Rhoads
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia
| | - Carol A Rauch
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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Ozer EA, Allen JP, Hauser AR. Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. BMC Genomics 2014; 15:737. [PMID: 25168460 PMCID: PMC4155085 DOI: 10.1186/1471-2164-15-737] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 08/22/2014] [Indexed: 12/11/2022] Open
Abstract
Background Pseudomonas aeruginosa is an important opportunistic pathogen responsible for many infections in hospitalized and immunocompromised patients. Previous reports estimated that approximately 10% of its 6.6 Mbp genome varies from strain to strain and is therefore referred to as “accessory genome”. Elements within the accessory genome of P. aeruginosa have been associated with differences in virulence and antibiotic resistance. As whole genome sequencing of bacterial strains becomes more widespread and cost-effective, methods to quickly and reliably identify accessory genomic elements in newly sequenced P. aeruginosa genomes will be needed. Results We developed a bioinformatic method for identifying the accessory genome of P. aeruginosa. First, the core genome was determined based on sequence conserved among the completed genomes of twelve reference strains using Spine, a software program developed for this purpose. The core genome was 5.84 Mbp in size and contained 5,316 coding sequences. We then developed an in silico genome subtraction program named AGEnt to filter out core genomic sequences from P. aeruginosa whole genomes to identify accessory genomic sequences of these reference strains. This analysis determined that the accessory genome of P. aeruginosa ranged from 6.9-18.0% of the total genome, was enriched for genes associated with mobile elements, and was comprised of a majority of genes with unknown or unclear function. Using these genomes, we showed that AGEnt performed well compared to other publically available programs designed to detect accessory genomic elements. We then demonstrated the utility of the AGEnt program by applying it to the draft genomes of two previously unsequenced P. aeruginosa strains, PA99 and PA103. Conclusions The P. aeruginosa genome is rich in accessory genetic material. The AGEnt program accurately identified the accessory genomes of newly sequenced P. aeruginosa strains, even when draft genomes were used. As P. aeruginosa genomes become available at an increasingly rapid pace, this program will be useful in cataloging the expanding accessory genome of this bacterium and in discerning correlations between phenotype and accessory genome makeup. The combination of Spine and AGEnt should be useful in defining the accessory genomes of other bacterial species as well. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-737) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University, 645 North Michigan Avenue, Suite 900, Chicago, IL 60611, USA.
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Abstract
Bacteria Pseudomonas aeruginosa, being opportunistic pathogens, are the major cause of nosocomial infections and, in some cases, the primary cause of death. They are virtually untreatable with currently known antibiotics. Phage therapy is considered as one of the possible approaches to the treatment of P. aeruginosa infections. Difficulties in the implementation of phage therapy in medical practice are related, for example, to the insufficient number and diversity of virulent phages that are active against P. aeruginosa. Results of interaction of therapeutic phages with bacteria in different conditions and environments are studied insufficiently. A little is known about possible interactions of therapeutic phages with resident prophages and plasmids in clinical strains in the foci of infections. This chapter highlights the different approaches to solving these problems and possible ways to expand the diversity of therapeutic P. aeruginosa phages and organizational arrangements (as banks of phages) to ensure long-term use of phages in the treatment of P. aeruginosa infections.
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Affiliation(s)
- Victor N Krylov
- Mechnikov Research Institute for Vaccines & Sera, Russian Academy of Medical Sciences, Moscow, Russia.
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Boon E, Meehan CJ, Whidden C, Wong DHJ, Langille MGI, Beiko RG. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev 2014; 38:90-118. [PMID: 23909933 PMCID: PMC4298764 DOI: 10.1111/1574-6976.12035] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/02/2013] [Accepted: 07/10/2013] [Indexed: 12/17/2022] Open
Abstract
A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term 'community' is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of 'Who is there?' and 'What are they doing?' to the mechanistically driven question of 'How will they respond?'
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Affiliation(s)
- Eva Boon
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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Lefeuvre P, Cellier G, Remenant B, Chiroleu F, Prior P. Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species. PLoS One 2013; 8:e63155. [PMID: 23723974 PMCID: PMC3665557 DOI: 10.1371/journal.pone.0063155] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/28/2013] [Indexed: 01/11/2023] Open
Abstract
Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.
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Affiliation(s)
- Pierre Lefeuvre
- CIRAD UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France.
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Varani AM, Monteiro-Vitorello CB, Nakaya HI, Van Sluys MA. The role of prophage in plant-pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:429-451. [PMID: 23725471 DOI: 10.1146/annurev-phyto-081211-173010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A diverse set of phage lineages is associated with the bacterial plant-pathogen genomes sequenced to date. Analysis of 37 genomes revealed 5,169 potential genes (approximately 4.3 Mbp) of phage origin, and at least 50% had no function assigned or are nonessential to phage biology. Some phytopathogens have transcriptionally active prophage genes under conditions that mimic plant infection, suggesting an association between plant disease and prophage transcriptional modulation. The role of prophages within genomes for cell biology varies. For pathogens such as Pectobacterium, Pseudomonas, Ralstonia, and Streptomyces, involvement of prophage in disease symptoms has been demonstrated. In Xylella and Xanthomonas, prophage activity is associated with genome rearrangements and strain differentiation. For other pathogens, prophage roles are yet to be established. This review integrates available information in a unique interface ( http://propnav.esalq.usp.br ) that may be assessed to improve research in prophage biology and its association with genome evolution and pathogenicity.
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Affiliation(s)
- Alessandro M Varani
- Departamento de Genética (LGN), Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900 Piracicaba/SP, Brazil
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Vercoe RB, Chang JT, Dy RL, Taylor C, Gristwood T, Clulow JS, Richter C, Przybilski R, Pitman AR, Fineran PC. Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet 2013; 9:e1003454. [PMID: 23637624 PMCID: PMC3630108 DOI: 10.1371/journal.pgen.1003454] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 03/02/2013] [Indexed: 12/26/2022] Open
Abstract
In prokaryotes, clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (Cas) proteins constitute a defence system against bacteriophages and plasmids. CRISPR/Cas systems acquire short spacer sequences from foreign genetic elements and incorporate these into their CRISPR arrays, generating a memory of past invaders. Defence is provided by short non-coding RNAs that guide Cas proteins to cleave complementary nucleic acids. While most spacers are acquired from phages and plasmids, there are examples of spacers that match genes elsewhere in the host bacterial chromosome. In Pectobacterium atrosepticum the type I-F CRISPR/Cas system has acquired a self-complementary spacer that perfectly matches a protospacer target in a horizontally acquired island (HAI2) involved in plant pathogenicity. Given the paucity of experimental data about CRISPR/Cas-mediated chromosomal targeting, we examined this process by developing a tightly controlled system. Chromosomal targeting was highly toxic via targeting of DNA and resulted in growth inhibition and cellular filamentation. The toxic phenotype was avoided by mutations in the cas operon, the CRISPR repeats, the protospacer target, and protospacer-adjacent motif (PAM) beside the target. Indeed, the natural self-targeting spacer was non-toxic due to a single nucleotide mutation adjacent to the target in the PAM sequence. Furthermore, we show that chromosomal targeting can result in large-scale genomic alterations, including the remodelling or deletion of entire pre-existing pathogenicity islands. These features can be engineered for the targeted deletion of large regions of bacterial chromosomes. In conclusion, in DNA-targeting CRISPR/Cas systems, chromosomal interference is deleterious by causing DNA damage and providing a strong selective pressure for genome alterations, which may have consequences for bacterial evolution and pathogenicity.
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Affiliation(s)
- Reuben B. Vercoe
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James T. Chang
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ron L. Dy
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Corinda Taylor
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Tamzin Gristwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James S. Clulow
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Corinna Richter
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rita Przybilski
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Andrew R. Pitman
- New Zealand Institute for Plant and Food Research, Christchurch, New Zealand
- Bio-Protection Research Centre, Lincoln University, Canterbury, New Zealand
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Krylov V, Shaburova O, Krylov S, Pleteneva E. A genetic approach to the development of new therapeutic phages to fight pseudomonas aeruginosa in wound infections. Viruses 2012; 5:15-53. [PMID: 23344559 PMCID: PMC3564109 DOI: 10.3390/v5010015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 12/03/2012] [Accepted: 12/12/2012] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa is a frequent participant in wound infections. Emergence of multiple antibiotic resistant strains has created significant problems in the treatment of infected wounds. Phage therapy (PT) has been proposed as a possible alternative approach. Infected wounds are the perfect place for PT applications, since the basic condition for PT is ensured; namely, the direct contact of bacteria and their viruses. Plenty of virulent ("lytic") and temperate ("lysogenic") bacteriophages are known in P. aeruginosa. However, the number of virulent phage species acceptable for PT and their mutability are limited. Besides, there are different deviations in the behavior of virulent (and temperate) phages from their expected canonical models of development. We consider some examples of non-canonical phage-bacterium interactions and the possibility of their use in PT. In addition, some optimal approaches to the development of phage therapy will be discussed from the point of view of a biologist, considering the danger of phage-assisted horizontal gene transfer (HGT), and from the point of view of a surgeon who has accepted the Hippocrates Oath to cure patients by all possible means. It is also time now to discuss the possible approaches in international cooperation for the development of PT. We think it would be advantageous to make phage therapy a kind of personalized medicine.
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Affiliation(s)
- Victor Krylov
- Laboratory for Bacteriophages Genetics. Mechnikov Research Institute of Vaccines and Sera, 5a Maliy Kazenniy per., Moscow, Russia.
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Morales-Espinosa R, Soberón-Chávez G, Delgado-Sapién G, Sandner-Miranda L, Méndez JL, González-Valencia G, Cravioto A. Genetic and phenotypic characterization of a Pseudomonas aeruginosa population with high frequency of genomic islands. PLoS One 2012; 7:e37459. [PMID: 22662157 PMCID: PMC3360775 DOI: 10.1371/journal.pone.0037459] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/20/2012] [Indexed: 11/23/2022] Open
Abstract
Various genomic islands, PAPI-1, PAPI-2, PAGI-1, PAGI-2, PAGI-3, and PAGI-4, and the element pKLC102 have been characterized in different P. aeruginosa strains from diverse habitats and geographical locations. Chromosomal DNA macroarray of 100 P. aeruginosa strains isolated from 85 unrelated patients hospitalized in an intensive care unit was created to assess the occurrence of these genomic islands (GEIs). The macroarray was then hybridized with labeled probes derived from each genomic island. In addition, PFGE patterns with SpeI, frequency of virulence genes, and antimicrobial resistance patterns of the strains were studied. Our results showed that almost all P. aeruginosa strains presented up to eight virulence genes. By SpeI macrorestriction fragment analysis we were able to identify 49 restriction patterns; 35 patterns correspond to single strains and the remaining 14 to strains subgroup (a-n). Most of the strains showed variation in number or composition of GEIs and a specific antimicrobial pattern indicating that each strain was an unrelated isolate. In terms of the number of genomic islands per strain, 7 GEIs were found in 34% of the strains, 6 in 18%, 5 in 12%, 4 in 14%, 3 in 10%, 2 in 7%, and 1 in 4%; only one isolate did not present any GEI. The genomic islands PAPI-1 and PAPI-2 and the element pKLC102 were the most frequently detected. The analysis of the location of each GEI in the chromosome of two strains show that the islands PAGI-3, PAPI-1, PAPI-2 and pKLC102 are present in the insertion site previously reported, but that PAGI-2 and PAGI-4 are inserted in another chromosome place in a site not characterized yet. In conclusion our data show that P. aeruginosa strains exhibited an epidemic population structure with horizontal transfer of DNA resulting in a high frequency of GEIs.
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Affiliation(s)
- Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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Vanga BR, Butler RC, Toth IK, Ronson CW, Pitman AR. Inactivation of PbTopo IIIβ causes hyper-excision of the Pathogenicity Island HAI2 resulting in reduced virulence of Pectobacterium atrosepticum. Mol Microbiol 2012; 84:648-63. [PMID: 22524709 DOI: 10.1111/j.1365-2958.2012.08050.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Topoisomerase III enzymes are present only in a limited set of bacteria and their physiological role remains unclear. Here, we show that PbTopo IIIβ, a homologue of topoisomerase III encoded on the chromosome of Pectobacterium atrosepticum strain SCRI1043 (Pba SCRI1043), is involved in excision of HAI2, a discrete ~100 kb region, from the Pba SCRI1043 chromosome. HAI2 is a Pathogenicity Island (PAI) that encodes coronafacic acid (Cfa), a major virulence determinant required for infection of potato. PAIs are horizontally acquired genetic elements that in some instances are able to excise from the chromosome of their host cell to form a circular episome prior to transfer to a recipient bacterium. We demonstrate excision of HAI2 from the chromosome, a process that is independent of growth phase and that results in the production of a circular intermediate. Inactivation of PbTopo IIIβ causes a 10(3) - to 10(4) -fold increase in excision, leading to reduced fitness in vitro and a decrease in the virulence of Pba SCRI1043 on potato. These results suggest that PbTopo IIIβ is required for stable maintenance of HAI2 in the chromosome of Pba SCRI1043 and may control as yet unidentified genes involved in viability and virulence of Pba SCRI1043 on potato.
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Affiliation(s)
- Bhanupratap R Vanga
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
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Genotypic and phenotypic variation in Pseudomonas aeruginosa reveals signatures of secondary infection and mutator activity in certain cystic fibrosis patients with chronic lung infections. Infect Immun 2011; 79:4802-18. [PMID: 21930755 DOI: 10.1128/iai.05282-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Evolutionary adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung is limited by genetic variation, which depends on rates of horizontal gene transfer and mutation supply. Because each may increase following secondary infection or mutator emergence, we sought to ascertain the incidence of secondary infection and genetic variability in populations containing or lacking mutators. Forty-nine strains collected over 3 years from 16 patients were phenotyped for antibiotic resistance and mutator status and were genotyped by repetitive-sequence PCR (rep-PCR), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Though phenotypic and genetic polymorphisms were widespread and clustered more strongly within than between longitudinal series, their distribution revealed instances of secondary infection. Sequence data, however, indicated that interlineage recombination predated initial strain isolation. Mutator series were more likely to be multiply antibiotic resistant, but not necessarily more variable in their nucleotide sequences, than nonmutators. One mutator and one nonmutator series were sequenced at mismatch repair loci and analyzed for gene content using DNA microarrays. Both were wild type with respect to mutL, but mutators carried an 8-bp mutS deletion causing a frameshift mutation. Both series lacked 126 genes encoding pilins, siderophores, and virulence factors whose inactivation has been linked to adaptation during chronic infection. Mutators exhibited loss of severalfold more genes having functions related to mobile elements, motility, and attachment. A 105-kb, 86-gene deletion was observed in one nonmutator that resulted in loss of virulence factors related to pyoverdine synthesis and elements of the multidrug efflux regulon. Diminished DNA repair activity may facilitate but not be absolutely required for rapid evolutionary change.
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Silby MW, Winstanley C, Godfrey SA, Levy SB, Jackson RW. Pseudomonasgenomes: diverse and adaptable. FEMS Microbiol Rev 2011; 35:652-80. [DOI: 10.1111/j.1574-6976.2011.00269.x] [Citation(s) in RCA: 578] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Boissy R, Ahmed A, Janto B, Earl J, Hall BG, Hogg JS, Pusch GD, Hiller LN, Powell E, Hayes J, Yu S, Kathju S, Stoodley P, Post JC, Ehrlich GD, Hu FZ. Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model. BMC Genomics 2011; 12:187. [PMID: 21489287 PMCID: PMC3094309 DOI: 10.1186/1471-2164-12-187] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 04/13/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is associated with a spectrum of symbiotic relationships with its human host from carriage to sepsis and is frequently associated with nosocomial and community-acquired infections, thus the differential gene content among strains is of interest. RESULTS We sequenced three clinical strains and combined these data with 13 publically available human isolates and one bovine strain for comparative genomic analyses. All genomes were annotated using RAST, and then their gene similarities and differences were delineated. Gene clustering yielded 3,155 orthologous gene clusters, of which 2,266 were core, 755 were distributed, and 134 were unique. Individual genomes contained between 2,524 and 2,648 genes. Gene-content comparisons among all possible S. aureus strain pairs (n = 136) revealed a mean difference of 296 genes and a maximum difference of 476 genes. We developed a revised version of our finite supragenome model to estimate the size of the S. aureus supragenome (3,221 genes, with 2,245 core genes), and compared it with those of Haemophilus influenzae and Streptococcus pneumoniae. There was excellent agreement between RAST's annotations and our CDS clustering procedure providing for high fidelity metabolomic subsystem analyses to extend our comparative genomic characterization of these strains. CONCLUSIONS Using a multi-species comparative supragenomic analysis enabled by an improved version of our finite supragenome model we provide data and an interpretation explaining the relatively larger core genome of S. aureus compared to other opportunistic nasopharyngeal pathogens. In addition, we provide independent validation for the efficiency and effectiveness of our orthologous gene clustering algorithm.
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Affiliation(s)
- Robert Boissy
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Pittsburgh, PA 15212, USA
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Abstract
BACKGROUND Chronic infections affect 17 million people yearly, and approximately 550,000 people die each year from, or with, their chronic infections. Acute and chornic infection differences are well known to clinicians, but the role of bacteria in producing these clinical differences remains poorly understood. METHODS This review relies on basic science, clinical studies, and a general review of the medical biofilm literature. The basic science studies are level A and B quality of evidence. The clinical studies are mainly retrospective cohort (level B) and case studies (level C). The biofilm literature includes reviews with varying levels of evidence. All articles have been peer reviewed and meet the standard of evidence-based medicine. RESULTS Acute infections are associated with planktonic bacteria and must be diagnosed rapidly and accurately to prevent tissue damage and/or death. In contrast, biofilm behavior pursues a more parasitic course by producing sustained host hyperinflammation, with the biofilm feeding on plasma exudate. Chronic infections vacillate over long periods of time, responding only partially to antibiotics and reemerging once the antibiotics are withdrawn. Chronic wounds exhibit similar clinical behavior seen in other chronic infections and are associated with biofilm phenotype bacteria on their surface. Biofilm infections, such as chronic wounds, cannot be adequately diagnosed with current clinical cultures; therefore, molecular methods are necessary. CONCLUSIONS Biofilm phenotype bacteria require multiple concurrent strategies, including débridement and targeted antibiofilm agents. Biofilm phenotype bacteria predominate on the surface of wounds, and biofilm-based management improves wound healing outcomes, indicating that biofilm is the right target for managing the bioburden barrier of chronic wounds.
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Ehrlich GD, Ahmed A, Earl J, Hiller NL, Costerton JW, Stoodley P, Post JC, DeMeo P, Hu FZ. The distributed genome hypothesis as a rubric for understanding evolution in situ during chronic bacterial biofilm infectious processes. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 2010; 59:269-79. [PMID: 20618850 PMCID: PMC2910629 DOI: 10.1111/j.1574-695x.2010.00704.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Most chronic infectious disease processes associated with bacteria are characterized by the formation of a biofilm that provides for bacterial attachment to the host tissue or the implanted medical device. The biofilm protects the bacteria from the host's adaptive immune response as well as predation by phagocytic cells. However, the most insidious aspect of biofilm biology from the host's point of view is that the biofilm provides an ideal setting for bacterial horizontal gene transfer (HGT). HGT provides for large-scale genome content changes in situ during the chronic infectious process. Obviously, for HGT processes to result in the reassortment of alleles and genes among bacterial strains, the infection must be polyclonal (polymicrobial) in nature. In this review, we marshal the evidence that all of the factors are present in biofilm infections to support HGT that results in the ongoing production of novel strains with unique combinations of genic characteristics and that the continual production of large numbers of novel, but related bacterial strains leads to persistence. This concept of an infecting population of bacteria undergoing mutagenesis to produce a 'cloud' of similar strains to confuse and overwhelm the host's immune system parallels genetic diversity strategies used by viral and parasitic pathogens.
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Affiliation(s)
- Garth D Ehrlich
- Center for Genomic Sciences, Allegheny Singer Research Institute, Pittsburgh, PA, USA.
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Pirnay JP, Bilocq F, Pot B, Cornelis P, Zizi M, Van Eldere J, Deschaght P, Vaneechoutte M, Jennes S, Pitt T, De Vos D. Pseudomonas aeruginosa population structure revisited. PLoS One 2009; 4:e7740. [PMID: 19936230 PMCID: PMC2777410 DOI: 10.1371/journal.pone.0007740] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 09/26/2009] [Indexed: 12/25/2022] Open
Abstract
At present there are strong indications that Pseudomonas aeruginosa exhibits an epidemic population structure; clinical isolates are indistinguishable from environmental isolates, and they do not exhibit a specific (disease) habitat selection. However, some important issues, such as the worldwide emergence of highly transmissible P. aeruginosa clones among cystic fibrosis (CF) patients and the spread and persistence of multidrug resistant (MDR) strains in hospital wards with high antibiotic pressure, remain contentious. To further investigate the population structure of P. aeruginosa, eight parameters were analyzed and combined for 328 unrelated isolates, collected over the last 125 years from 69 localities in 30 countries on five continents, from diverse clinical (human and animal) and environmental habitats. The analysed parameters were: i) O serotype, ii) Fluorescent Amplified-Fragment Length Polymorphism (FALFP) pattern, nucleotide sequences of outer membrane protein genes, iii) oprI, iv) oprL, v) oprD, vi) pyoverdine receptor gene profile (fpvA type and fpvB prevalence), and prevalence of vii) exoenzyme genes exoS and exoU and viii) group I pilin glycosyltransferase gene tfpO. These traits were combined and analysed using biological data analysis software and visualized in the form of a minimum spanning tree (MST). We revealed a network of relationships between all analyzed parameters and non-congruence between experiments. At the same time we observed several conserved clones, characterized by an almost identical data set. These observations confirm the nonclonal epidemic population structure of P. aeruginosa, a superficially clonal structure with frequent recombinations, in which occasionally highly successful epidemic clones arise. One of these clones is the renown and widespread MDR serotype O12 clone. On the other hand, we found no evidence for a widespread CF transmissible clone. All but one of the 43 analysed CF strains belonged to a ubiquitous P. aeruginosa "core lineage" and typically exhibited the exoS(+)/exoU(-) genotype and group B oprL and oprD alleles. This is to our knowledge the first report of an MST analysis conducted on a polyphasic data set.
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Affiliation(s)
- Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Burn Centre, Queen Astrid Military Hospital, Brussel, Belgium.
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Abstract
Biofilms probably induce a chronic and/or 'quiet' inflammation in the chronic wound and so delay healing. This paper reviews current strategies that can be used to suppress biofilms in chronic wounds until better options are available.
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Affiliation(s)
- D D Rhoads
- Southwest Regional Wound Care Center, Lubbock, Texas, USA
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